Prokaryotic mRNA is most of the times polycistronic, while the eukaryotic mRNA is monocistronic. The 5′-7 methyl guanosine is absent in prokaryotes, while in eukaryotes is present.
3′ poly A tail is absent on prokaryotes, while in eukaryotes it is not. Furthemore, the Ribosome Binding Site (Shine Dalgarno Sequence) is only present on prokaryotes. Also on prokaryotes, the mRNA consists of an exact transcribed copy of DNA, while in eukaryotes mRNA is more elaborate. The prokaryotic mRNA degrades easier, while the eukaryotic one is more stable due to the cap structure and polyA tail. Eukaryotic mRNA is composed of small templates of the original gene that is cleaved and rejoined by assistance of pre-mRNA. Their similarities include the fact they contain the same nucleotides and use the same start codon AUG. The codons needed for the termination of the translation are also the same: UAG,UGA,UAA. There are differences in the mode of translation initiation in prokaryotes and eukaryotes. The inititation codon is AUG in eukaryotes. Also in 5′ side of eukaryotes, a specific purine-rich sequence is not used for separation of the initiator AUG from the internal ones. Generally the AUG near the 5′ end plays the role of the initiator in eukaryotes assisted by the 40S ribosome that binds the 5′ end and moves toward the 3′ direction to search the AUG codon and by the helicases that hdrolyze ATP. When the Met-tRNAi joins the AUG codon the process can begin. On the other hand in the prokaryotes, mRNA has several Shine-Dalgarno sequences that serve as start sites and therefore several proteins can be synthesized compared to the eukaryotes that have one start site only and act as a template for a single protein. Initiation mechanism major difference between prokaryotes and eukaryotes is that the 5′ end of the mRNA is aavailable for the robosomes of the prokaryotes after the transcription state. While in eukaryotes, the pre-mRNA has to be processed and transported toward the cytoplasm before the translation starts. On the other hand those processes are similar in both of them as they both employ the same core mechanism, with three common factors(IF-1-3) .